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Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models

By Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh and Glynn Winskel

Abstract

International audienceIn this paper, we introduce a novel way of constructing concise causal histories (pathways) to represent how specified structures are formed during simulation of systems represented by rule- based models. This is founded on a new, clean, graph-based semantics introduced in the first part of this paper for Kappa, a rule-based modelling language that has emerged as a natural description of protein-protein interactions in molecular biology [1]. The semantics is capable of capturing the whole of Kappa, including subtle side-effects on deletion of structure, and its structured presentation provides the basis for the translation of techniques to other models. In particular, we give a notion of trajectory compression, which restricts a trace culminating in the production of a given structure to the actions necessary for the structure to occur. This is central to the reconstruction of biochemical pathways due to the failure of traditional techniques to provide adequately concise causal histories, and we expect it to be applicable in a range of other modelling situations

Topics: concurrency, rule-based models, graph rewriting, pathways, causality, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, [ INFO.INFO-PL ] Computer Science [cs]/Programming Languages [cs.PL], [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Publisher: HAL CCSD
Year: 2012
DOI identifier: 10.4230/LIPIcs.FSTTCS.2012.276
OAI identifier: oai:HAL:hal-00809065v1
Provided by: Hal-Diderot

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